feat: separator for gene list or hpo terms (#1196) (#1480)

varfish-org · Mar 25, 2024 · ba73b99 · ba73b99
1 parent 64e979a
commit ba73b99
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Showing 4 changed files with 20 additions and 17 deletions.
diff --git a/svs/vueapp/src/components/SvFilterForm/GenesRegionsPane.vue b/svs/vueapp/src/components/SvFilterForm/GenesRegionsPane.vue
@@ -374,14 +374,15 @@ defineExpose({
           ref="geneAllowListRegionTextareaRef"
           v-model="props.querySettings.gene_allowlist"
           :validate="validateGeneBatch"
+          :tokenize="/([^\s;,]+)/g"
         />
         <small class="form-text">
           Enter a list of genes to restrict your query to, separated with
-          spaces. You can use gene symbols, HGNC ids, ENSEMBL gene IDs, or
-          Entrez Gene IDs. For example, all of the following code for TGDS
-          (TDP-glucose 4,6-dehydratase): <code>TGDS</code>,
-          <code>HGNC:20324</code>, <code>ENSG00000088451</code>,
-          <code>23483</code>.
+          spaces, tabs, <code>;</code> or <code>,</code>. You can use gene
+          symbols, HGNC ids, ENSEMBL gene IDs, or Entrez Gene IDs. For example,
+          all of the following code for TGDS (TDP-glucose 4,6-dehydratase):
+          <code>TGDS</code>, <code>HGNC:20324</code>,
+          <code>ENSG00000088451</code>, <code>23483</code>.
         </small>
       </div>
     </div>

diff --git a/variants/vueapp/src/components/FilterForm/GenesRegionsPane.vue b/variants/vueapp/src/components/FilterForm/GenesRegionsPane.vue
@@ -378,14 +378,15 @@ defineExpose({
           ref="geneAllowListRegionTextareaRef"
           v-model="props.querySettings.gene_allowlist"
           :validate="validateGeneBatch"
+          :tokenize="/([^\s;,]+)/g"
         />
         <small class="form-text">
-          Enter a list of genes to restrict your query to, separated with
-          spaces. You can use gene symbols, HGNC ids, ENSEMBL gene IDs, or
-          Entrez Gene IDs. For example, all of the following code for TGDS
-          (TDP-glucose 4,6-dehydratase): <code>TGDS</code>,
-          <code>HGNC:20324</code>, <code>ENSG00000088451</code>,
-          <code>23483</code>.
+          Enter a list of genes to restrict your query to, separated by spaces,
+          tabs, <code>;</code> or <code>,</code>. You can use gene symbols, HGNC
+          ids, ENSEMBL gene IDs, or Entrez Gene IDs. For example, all of the
+          following code for TGDS (TDP-glucose 4,6-dehydratase):
+          <code>TGDS</code>, <code>HGNC:20324</code>,
+          <code>ENSG00000088451</code>, <code>23483</code>.
         </small>
       </div>
     </div>

diff --git a/variants/vueapp/src/components/HpoTermInput.vue b/variants/vueapp/src/components/HpoTermInput.vue
@@ -82,13 +82,14 @@ const refreshTextValue = async (termsArray) => {
 
 /** Refresh model value from text value. */
 const refreshModelValue = () => {
-  const regex = /(HP:\d{7}|OMIM:\d{6}|DECIPHER:\d+|ORPHA:\d+)( - [^;]+)?(;|$)/g
+  const regex =
+    /(HP:\d{7}|OMIM:\d{6}|DECIPHER:\d+|ORPHA:\d+)( - [^;,]+)?(;|,|$)/g
   const cleanTextValue = (textValue.value || '')
-    .replace(/^\s*;?\s*|\s*;?\s*$/g, '') // replace any cruft in beginning or end of the string
+    .replace(/^\s*[;,]?\s*|\s*[;,]?\s*$/g, '') // replace any cruft in beginning or end of the string
     .replace(/\s{2,}/g, ' ') // replace double (or more) spaces with one space
-    .replace(/[;\s]{2,}/g, '; ') // replace any sequence of multiple ; and spaces with `; `
-    .replace(/;([^\s$])/g, '; $1') // add missing space after semicolon
-    .replace(/([^;])\s(HP|OMIM|DECIPHER|ORPHA):/g, '$1; $2:') // set missing semicolons in front of HPO id
+    .replace(/[;,\s]{2,}/g, '; ') // replace any sequence of multiple ; and spaces with `; `
+    .replace(/[;,]([^\s$])/g, '; $1') // add missing space after semicolon
+    .replace(/([^;,])\s(HP|OMIM|DECIPHER|ORPHA):/g, '$1; $2:') // set missing semicolons in front of HPO id
   const hpoSelected = []
   let result
   while ((result = regex.exec(cleanTextValue))) {

diff --git a/variants/vueapp/src/components/TokenizingTextarea.vue b/variants/vueapp/src/components/TokenizingTextarea.vue
@@ -32,7 +32,7 @@ const props = defineProps({
    * other - tokenize based on whitespace
    */
   // eslint-disable-next-line vue/require-default-prop
-  tokenize: Function,
+  tokenize: RegExp,
   /**
    * Definition on token validation
    *